This series of files compile all analyses done during Chapter 2:

All analyses have been done with R 3.6.3.

Click on the table of contents in the left margin to assess a specific analysis.
Click on a figure to zoom it

Sources of activity considered for the analyses:

Fisheries data considered for the analyses (expressed as number of fishing events or kilograms of collected individuals for each gear):

Gear Code Years Events Species
Trap TrapFish 2010-2015 1061 Buccinum sp., Cancer irroratus, Chionoecetes opilio, Homarus americanus
Bottom-trawl TrawFish 2013-2014 2 Pandalus borealis
Net NetFish 2010 5 Clupea harengus, Gadus morhua
Dredge DredFish 2010-2014 21 Mactromeris polynyma

1. Explorations

1.1. Correlations between all variables

Correlations have been calculated with Spearman’s rank coefficient.

Correlation coefficients between habitat parameters and metals concentrations
  om gravel sand silt clay arsenic cadmium chromium copper iron manganese mercury lead zinc S N H J aquaculture city dredging_collect dredging_dump industry shipping_mooring shipping_traffic sewers_rain sewers_waste wharves_city wharves_industry fisheries_trap fisheries_trawl fisheries_net fisheries_dredge cumulative_influence
om 1 -0.379 -0.708 0.68 0.023 0.57 0.486 0.606 0.593 0.586 0.568 0.537 0.587 0.605 -0.026 -0.121 0.122 0.136 -0.41 -0.033 0.22 0.43 0.309 0.518 0.291 0.239 0.401 -0.073 0.366 -0.508 -0.213 0.004 -0.238 0.274
gravel -0.379 1 0.186 -0.471 0.099 -0.127 -0.23 -0.194 -0.23 -0.232 -0.199 -0.207 -0.169 -0.235 0.029 0.007 0.012 0.07 0.143 -0.068 -0.175 -0.161 -0.081 -0.216 -0.02 0 -0.073 -0.061 -0.166 0.16 0.172 -0.055 0.068 -0.12
sand -0.708 0.186 1 -0.788 -0.308 -0.648 -0.504 -0.587 -0.483 -0.407 -0.524 -0.611 -0.588 -0.529 0.059 0.084 0.031 -0.027 0.433 0.279 -0.002 -0.17 -0.102 -0.42 -0.169 -0.31 -0.468 0.324 -0.17 0.428 0.087 -0.158 0.246 -0.058
silt 0.68 -0.471 -0.788 1 0.05 0.548 0.482 0.506 0.441 0.362 0.449 0.566 0.519 0.493 -0.054 -0.013 -0.068 -0.055 -0.409 -0.15 0.046 0.179 0.079 0.424 0.083 0.247 0.391 -0.196 0.175 -0.385 -0.18 0.119 -0.241 0.076
clay 0.023 0.099 -0.308 0.05 1 0.208 0.095 0.129 0.11 0.062 0.144 0.052 0.15 0.107 -0.098 -0.076 -0.044 0.02 -0.059 -0.02 0.025 0.015 0.02 0.006 0.012 0.241 0.238 -0.031 0.037 -0.096 -0.104 0.191 -0.046 0.066
arsenic 0.57 -0.127 -0.648 0.548 0.208 1 0.797 0.862 0.791 0.656 0.78 0.707 0.902 0.87 -0.266 -0.149 -0.193 0.008 -0.657 -0.067 0.06 0.216 0.076 0.66 0.214 0.522 0.709 -0.158 0.213 -0.444 -0.237 0.078 -0.466 0.181
cadmium 0.486 -0.23 -0.504 0.482 0.095 0.797 1 0.818 0.694 0.564 0.717 0.75 0.886 0.853 -0.308 -0.042 -0.291 -0.133 -0.783 -0.015 -0.002 0.186 -0.084 0.728 0.039 0.468 0.701 -0.14 0.142 -0.345 -0.306 -0.001 -0.46 0.111
chromium 0.606 -0.194 -0.587 0.506 0.129 0.862 0.818 1 0.909 0.818 0.917 0.753 0.92 0.939 -0.331 -0.167 -0.273 -0.041 -0.73 -0.02 0.263 0.437 0.103 0.733 0.344 0.596 0.763 -0.103 0.409 -0.323 -0.349 0.055 -0.559 0.362
copper 0.593 -0.23 -0.483 0.441 0.11 0.791 0.694 0.909 1 0.808 0.842 0.715 0.872 0.952 -0.298 -0.172 -0.225 -0.025 -0.655 0.238 0.438 0.571 0.219 0.752 0.432 0.641 0.755 0.169 0.536 -0.319 -0.451 0.033 -0.602 0.553
iron 0.586 -0.232 -0.407 0.362 0.062 0.656 0.564 0.818 0.808 1 0.878 0.461 0.664 0.785 -0.377 -0.273 -0.251 0.034 -0.616 0.114 0.508 0.652 0.325 0.671 0.624 0.578 0.674 0.061 0.644 -0.292 -0.368 0.055 -0.648 0.596
manganese 0.568 -0.199 -0.524 0.449 0.144 0.78 0.717 0.917 0.842 0.878 1 0.658 0.798 0.846 -0.287 -0.096 -0.261 -0.085 -0.758 -0.02 0.422 0.557 0.209 0.769 0.497 0.671 0.822 -0.082 0.562 -0.301 -0.466 0.106 -0.649 0.493
mercury 0.537 -0.207 -0.611 0.566 0.052 0.707 0.75 0.753 0.715 0.461 0.658 1 0.845 0.755 -0.234 -0.084 -0.199 -0.075 -0.724 -0.064 0.053 0.237 -0.043 0.731 0.133 0.509 0.703 -0.142 0.196 -0.356 -0.314 0.01 -0.42 0.168
lead 0.587 -0.169 -0.588 0.519 0.15 0.902 0.886 0.92 0.872 0.664 0.798 0.845 1 0.939 -0.304 -0.135 -0.252 -0.051 -0.707 0.029 0.129 0.316 0.05 0.739 0.211 0.599 0.769 -0.065 0.277 -0.376 -0.307 0.036 -0.475 0.275
zinc 0.605 -0.235 -0.529 0.493 0.107 0.87 0.853 0.939 0.952 0.785 0.846 0.755 0.939 1 -0.32 -0.145 -0.253 -0.056 -0.718 0.152 0.307 0.471 0.151 0.791 0.341 0.603 0.764 0.067 0.429 -0.359 -0.397 0.026 -0.578 0.431
S -0.026 0.029 0.059 -0.054 -0.098 -0.266 -0.308 -0.331 -0.298 -0.377 -0.287 -0.234 -0.304 -0.32 1 0.561 0.705 -0.052 0.348 -0.141 -0.113 -0.158 0.077 -0.255 -0.045 -0.315 -0.33 -0.069 -0.151 0.079 0.217 -0.112 0.335 -0.164
N -0.121 0.007 0.084 -0.013 -0.076 -0.149 -0.042 -0.167 -0.172 -0.273 -0.096 -0.084 -0.135 -0.145 0.561 1 -0.041 -0.683 -0.005 -0.061 -0.139 -0.163 -0.169 -0.023 -0.111 -0.116 -0.067 -0.061 -0.169 0.183 -0.008 -0.137 0.029 -0.133
H 0.122 0.012 0.031 -0.068 -0.044 -0.193 -0.291 -0.273 -0.225 -0.251 -0.261 -0.199 -0.252 -0.253 0.705 -0.041 1 0.598 0.373 -0.087 0.026 -0.014 0.285 -0.243 -0.028 -0.306 -0.328 -0.004 -0.015 -0.058 0.163 -0.035 0.425 -0.089
J 0.136 0.07 -0.027 -0.055 0.02 0.008 -0.133 -0.041 -0.025 0.034 -0.085 -0.075 -0.051 -0.056 -0.052 -0.683 0.598 1 0.186 0.01 0.073 0.054 0.236 -0.128 -0.021 -0.105 -0.146 0.034 0.061 -0.168 0.033 0.127 0.23 -0.014
aquaculture -0.41 0.143 0.433 -0.409 -0.059 -0.657 -0.783 -0.73 -0.655 -0.616 -0.758 -0.724 -0.707 -0.718 0.348 -0.005 0.373 0.186 1 -0.069 -0.168 -0.306 0.128 -0.827 -0.183 -0.597 -0.839 0.079 -0.271 0.282 0.594 0.02 0.722 -0.233
city -0.033 -0.068 0.279 -0.15 -0.02 -0.067 -0.015 -0.02 0.238 0.114 -0.02 -0.064 0.029 0.152 -0.141 -0.061 -0.087 0.01 -0.069 1 0.292 0.369 0.051 0.299 0.133 0.324 0.162 0.969 0.255 -0.097 -0.401 -0.012 -0.424 0.564
dredging_collect 0.22 -0.175 -0.002 0.046 0.025 0.06 -0.002 0.263 0.438 0.508 0.422 0.053 0.129 0.307 -0.113 -0.139 0.026 0.073 -0.168 0.292 1 0.895 0.734 0.359 0.741 0.485 0.416 0.371 0.946 0.012 -0.507 0.028 -0.366 0.849
dredging_dump 0.43 -0.161 -0.17 0.179 0.015 0.216 0.186 0.437 0.571 0.652 0.557 0.237 0.316 0.471 -0.158 -0.163 -0.014 0.054 -0.306 0.369 0.895 1 0.723 0.588 0.805 0.545 0.521 0.436 0.956 -0.173 -0.465 -0.048 -0.518 0.924
industry 0.309 -0.081 -0.102 0.079 0.02 0.076 -0.084 0.103 0.219 0.325 0.209 -0.043 0.05 0.151 0.077 -0.169 0.285 0.236 0.128 0.051 0.734 0.723 1 0.183 0.656 0.17 0.146 0.17 0.765 -0.172 -0.09 -0.086 -0.041 0.61
shipping_mooring 0.518 -0.216 -0.42 0.424 0.006 0.66 0.728 0.733 0.752 0.671 0.769 0.731 0.739 0.791 -0.255 -0.023 -0.243 -0.128 -0.827 0.299 0.359 0.588 0.183 1 0.41 0.592 0.766 0.24 0.5 -0.417 -0.597 -0.05 -0.728 0.543
shipping_traffic 0.291 -0.02 -0.169 0.083 0.012 0.214 0.039 0.344 0.432 0.624 0.497 0.133 0.211 0.341 -0.045 -0.111 -0.028 -0.021 -0.183 0.133 0.741 0.805 0.656 0.41 1 0.568 0.451 0.232 0.834 -0.005 -0.181 0.097 -0.521 0.825
sewers_rain 0.239 0 -0.31 0.247 0.241 0.522 0.468 0.596 0.641 0.578 0.671 0.509 0.599 0.603 -0.315 -0.116 -0.306 -0.105 -0.597 0.324 0.485 0.545 0.17 0.592 0.568 1 0.892 0.279 0.571 -0.07 -0.509 0.209 -0.747 0.661
sewers_waste 0.401 -0.073 -0.468 0.391 0.238 0.709 0.701 0.763 0.755 0.674 0.822 0.703 0.769 0.764 -0.33 -0.067 -0.328 -0.146 -0.839 0.162 0.416 0.521 0.146 0.766 0.451 0.892 1 0.069 0.523 -0.257 -0.569 0.061 -0.75 0.522
wharves_city -0.073 -0.061 0.324 -0.196 -0.031 -0.158 -0.14 -0.103 0.169 0.061 -0.082 -0.142 -0.065 0.067 -0.069 -0.061 -0.004 0.034 0.079 0.969 0.371 0.436 0.17 0.24 0.232 0.279 0.069 1 0.331 -0.042 -0.34 0.016 -0.35 0.632
wharves_industry 0.366 -0.166 -0.17 0.175 0.037 0.213 0.142 0.409 0.536 0.644 0.562 0.196 0.277 0.429 -0.151 -0.169 -0.015 0.061 -0.271 0.255 0.946 0.956 0.765 0.5 0.834 0.571 0.523 0.331 1 -0.094 -0.454 0.037 -0.497 0.9
fisheries_trap -0.508 0.16 0.428 -0.385 -0.096 -0.444 -0.345 -0.323 -0.319 -0.292 -0.301 -0.356 -0.376 -0.359 0.079 0.183 -0.058 -0.168 0.282 -0.097 0.012 -0.173 -0.172 -0.417 -0.005 -0.07 -0.257 -0.042 -0.094 1 0.226 0.132 0.145 -0.075
fisheries_trawl -0.213 0.172 0.087 -0.18 -0.104 -0.237 -0.306 -0.349 -0.451 -0.368 -0.466 -0.314 -0.307 -0.397 0.217 -0.008 0.163 0.033 0.594 -0.401 -0.507 -0.465 -0.09 -0.597 -0.181 -0.509 -0.569 -0.34 -0.454 0.226 1 -0.071 0.513 -0.458
fisheries_net 0.004 -0.055 -0.158 0.119 0.191 0.078 -0.001 0.055 0.033 0.055 0.106 0.01 0.036 0.026 -0.112 -0.137 -0.035 0.127 0.02 -0.012 0.028 -0.048 -0.086 -0.05 0.097 0.209 0.061 0.016 0.037 0.132 -0.071 1 -0.08 0.077
fisheries_dredge -0.238 0.068 0.246 -0.241 -0.046 -0.466 -0.46 -0.559 -0.602 -0.648 -0.649 -0.42 -0.475 -0.578 0.335 0.029 0.425 0.23 0.722 -0.424 -0.366 -0.518 -0.041 -0.728 -0.521 -0.747 -0.75 -0.35 -0.497 0.145 0.513 -0.08 1 -0.617
cumulative_influence 0.274 -0.12 -0.058 0.076 0.066 0.181 0.111 0.362 0.553 0.596 0.493 0.168 0.275 0.431 -0.164 -0.133 -0.089 -0.014 -0.233 0.564 0.849 0.924 0.61 0.543 0.825 0.661 0.522 0.632 0.9 -0.075 -0.458 0.077 -0.617 1

According to these results, many variables are correlated (\(|\rho|\) > 0.80). We can group abiotic parameters to reduce multicolinearity in the following SDM, but not for influence indices as we need to consider them all. Based on these coefficients, we can regroup:

  • organic matter and sand (sand deleted)
  • arsenic, chromium, lead and zinc (chromium, lead and zinc deleted)

1.2. Relationships between indices and parameters

This section explores relationships between human activity exposure indices (dependant variables) and biotic and abiotic parameters (predictors).

Several types of models were considered to explore relationships: linear, quadratic, exponential and logarithmic. The model with the highest \(R^{2}\) is presented on each plot. Only linear models were implemented, as there are some bugs with the calculation of the others.

AquaInf

CityInf

InduInf

CollDred

DumpDred

MoorShip

TrafShip

RainSew

WastSew

CityWha

InduWha

TrapFish

TrawFish

NetFish

DredFish

Cumulative Influence

1.3. Species abundances by cumulative influence index

Let’s have a look at the distribution of species phyla along the gradient of cumulative influence.

Phylum mean abundances by group
Phylum low bad moderate high good
Annelida NA 29.5 32.3 19.7 NA
Arthropoda NA 20.3 50.6 26.3 NA
Cnidaria NA 0.1 0 0 NA
Echinodermata NA 13.5 1.32 5.12 NA
Mollusca NA 10.8 13.5 15.9 NA
Nematoda NA 22.7 9.95 0.0625 NA
Nemertea NA 0 0.195 0 NA
Sipuncula NA 0 0.268 0.438 NA

2. Species Distribution Modelling

The aim here is to predict the structure of benthic communities based on the values of environmental variables.

We will use abiotic parameters and the indices of human influence (calculated in Section 1) as predictors. We tested different methods: GLMs, GAMs, Random Forest and HMSC. Each method has been developed in dedicated scripts, whose final objects were imported here to present results and trends.

For each method, results are presented with a table regrouping McFadden’s or Tjur’s pseudo-R2, validation ratios and variables coefficients, and with maps displaying the probability of presence of each taxon for which the pseudo-R2 is higher than 0.20 (and different than 1). The raster presents results of the SDM (grey: low probability, dark blue: high). Stations are either plotted with colors (green = taxa present, red = taxon absent) or with circles (wider circcles = higher taxon density).

2.1. Generalized Linear Models

Diagnostics for each model can be found here.

Presence/absence data

Here, we considered presence/absence data with a binomial distribution.

Abiotic parameters
McFadden’s pseudo-R2, match ratios and variables coefficients for each taxon
  Pseudo-R2 intercept om gravel silt clay arsenic cadmium copper iron manganese mercury
aceroides_aceroides_latipes 0.22 -10.3 0.701 -32.6 -1.06 -0.492 -0.584 -0.107 0.799 -2.04 0.665 0.569
akanthophoreus_gracilis 0.22 -1.77 0.72 -0.256 -0.317 -2.08 1.78 -1.2 -0.452 -1.12 -0.58 0.669
ameritella_agilis 0.28 -4.76 -0.225 0.381 0.471 -0.0246 1.12 1.56 -0.507 0.674 -5.38 -0.717
ameroculodes_edwardsi 0.39 -314 1.65 0.307 -0.361 -1687 0.644 -0.774 0.782 -1.1 -4.3 -0.374
ampelisca_vadorum 1 -139 23.8 16.8 -5.39 -85.7 28.2 -50.2 -11 -9.73 25 -36.3
amphipoda 0.06 -0.634 0.253 0.141 -0.0772 0.277 0.41 0.166 -0.15 -0.543 0.176 0.202
anonyx_lilljeborgi 0.12 -2.59 0.064 -0.213 -0.381 -0.0595 -0.538 -0.465 -0.364 -0.968 1.03 0.00569
anthozoa 0 -26.6 9.71e-15 -2.81e-15 -9.5e-15 6.06e-15 5.66e-15 2.43e-15 -1.26e-14 4.18e-15 -7.2e-15 8.98e-15
arcteobia_anticostiensis 1 -157 -9.45 1.88 25.7 3.61 -99.4 46.6 7.77 5.16 -96.3 -33.5
arrhoges_occidentalis 1 -698 -308 -46.1 216 -836 -55.9 -14 63.8 -219 130 -344
astarte_sp 0.49 -363 -1.47 -1.02 -1.46 -1941 2.28 -2.47 3.35 -0.149 -7.68 0.84
axinopsida_orbiculata 0.15 -350 0.179 0.145 0.459 -1899 0.175 0.491 -0.0483 0.0278 -0.52 -1.75
axiothella_catenata 1 -125 48.3 4.67 15.1 29.5 -98.2 6.72 30.9 -96.1 19.6 13.8
bathymedon_longimanus 0.75 -45.8 -0.956 -16.6 3.38 -66.1 -19.9 7.02 2.35 0.891 -18.4 -11.6
bathymedon_obtusifrons -12.23 -3.3e+15 -1.49e+15 7.24e+14 1.38e+15 -7.53e+14 -1.75e+15 6.27e+14 1.94e+15 -4.87e+14 -5.42e+14 -6.12e+14
bipalponephtys_neotena 0.34 2.73 3.35 0.149 0.0756 0.191 -0.593 0.233 -0.634 -0.492 0.406 -0.187
boreochiton_ruber 0.61 -416 -14.2 0.61 3.38 -2147 -9.39 1.35 4.62 -1.69 -4.8 -5.78
brachydiastylis_sp 0.56 -259 -4.99 1.19 3.89 -1353 1.93 -1.36 -1.3 -0.242 2.17 -6.95
byblis_gaimardii 0.3 -314 0.0612 0.387 -0.109 -1687 0.906 -0.653 -1.42 -0.56 -0.422 -0.415
cancer_irroratus 1 -512 -262 86.7 75.8 43.8 54.4 230 104 -257 -192 -14.6
caprella_septentrionalis 0.63 -15.3 -4.19 2.21 -2.77 3.99 -6.9 7.77 11.1 -15.9 0.0592 1.47
chaetodermatida 0.15 -3.61 -0.0259 -0.529 -0.183 -7.93 0.119 -0.603 0.494 -0.493 -0.957 0.087
chionoecetes_opilio -6.59 -2.54e+15 9.98e+13 8.09e+13 1.36e+15 -2.07e+15 -4.63e+14 -3.6e+14 -9.33e+13 -3.85e+14 8.51e+14 -1.17e+15
chlamys_islandica 1 -183 -134 -4.48 64.1 -106 5.14 -40.8 62.6 9.69 -19.2 -69.4
chone_sp 1 -646 -267 -134 19.7 1.93 -116 303 422 -593 -137 60.2
ciliatocardium_ciliatum 1 -265 169 -8.55 -257 236 92.7 -68.4 83.8 -85.6 -162 51.1
cirripedia 1 -44.2 -2.64 1.01 -3.93 6.16 -8.43 5.17 -13.3 -0.0516 18.4 -5.74
cistenides_granulata 0.21 -2.35 0.326 0.0192 -0.312 -1.3 0.612 -0.313 -1.44 -0.267 -0.162 0.134
cossura_longocirrata 1 -1045 -204 335 749 134 -28.5 361 -190 392 -120 26.9
crassicorophium_bonellii 0.59 -273 -2.76 -0.438 1.55 -1450 0.901 -2.44 -0.651 -2.1 5.2 -3
crenella_decussata 0.78 -29.8 -13.5 3.57 2.27 5.28 -15.1 0.328 2.79 1.54 -10.6 -6.1
cumacea 0.17 -128 -0.618 -30.3 -0.344 -627 0.362 -0.956 0.167 -0.652 1.86 -0.542
cyclocardia_borealis 0 -26.6 9.71e-15 -2.81e-15 -9.5e-15 6.06e-15 5.66e-15 2.43e-15 -1.26e-14 4.18e-15 -7.2e-15 8.98e-15
cyrtodaria_siliqua 1 -748 -389 -92.1 31.2 126 -264 124 165 86 -288 -321
diastylis_rathkei 0.3 -4.08 -2.19 1.09 2.62 -1.3 -1.44 -0.453 0.895 0.85 1.02 -1.93
diastylis_sculpta 0.39 -5.76 -2.69 -0.37 2.21 -0.912 -2.92 -1.7 3.98 -0.997 0.224 -2.19
diastylis_sp 0.57 -26.8 1.92 -14.4 3.14 -60 -3.08 1.47 -0.572 0.875 -5.51 -3.01
echinarachnius_parma 0.62 -18.9 -6.29 0.0261 3.29 0.621 -17.8 2.07 2.69 1.32 -7.79 -5.6
edotia_montosa 1 -147 144 -53 -168 124 -43.5 33.2 45.8 -118 105 -63.9
ennucula_tenuis 0.29 -0.407 1.06 0.242 0.202 -0.866 2.11 -2.32 0.0303 -0.0814 -2.15 1.1
eteone_sp 0.19 -370 -2.12 0.425 0.902 -1998 0.306 -0.623 0.896 0.209 -0.398 -0.223
euchone_sp -12.23 -3.3e+15 -1.49e+15 7.24e+14 1.38e+15 -7.53e+14 -1.75e+15 6.27e+14 1.94e+15 -4.87e+14 -5.42e+14 -6.12e+14
eudorella_emarginata 0.41 -258 -0.0962 1.32 2.36 -1383 -0.181 1.1 -0.138 -0.151 -0.0414 0.629
eudorellopsis_integra 0.42 -7.42 2.73 -0.449 -0.512 -45.4 0.6 -0.891 -1.54 -1.09 1.96 0.588
euspira_pallida 0.3 -110 -1.75 -27.2 1.67 -521 0.638 -1.96 1.82 -1.49 -0.54 -2.49
glycera_capitata 1 -109 -74.7 32.4 37.1 13.8 -26.7 13.5 47.5 15.7 -23.7 16.8
glycera_sp 0.61 -28.5 -17 8.45 10.7 -3.52 -10 14.6 19 -20.3 -2.11 2.27
goniada_maculata 0.23 -361 0.843 -1.18 -0.0669 -1966 0.587 -0.181 -0.932 -0.154 -0.592 0.273
guernea_prinassus_nordenskioldi 0 -26.6 9.71e-15 -2.81e-15 -9.5e-15 6.06e-15 5.66e-15 2.43e-15 -1.26e-14 4.18e-15 -7.2e-15 8.98e-15
halacaridae_spp 1 -183 -134 -4.48 64.1 -106 5.14 -40.8 62.6 9.69 -19.2 -69.4
haminoea_solitaria 0.4 -28.3 2.88 -26 -1.79 -48.6 -1.19 1.98 -0.646 -2.9 -4.97 -3.97
hardametopa_carinata -12.23 -3.3e+15 -1.49e+15 7.24e+14 1.38e+15 -7.53e+14 -1.75e+15 6.27e+14 1.94e+15 -4.87e+14 -5.42e+14 -6.12e+14
harmothoe_sp 0.31 -297 -1.35 1.75 3.21 -1593 -0.813 -0.895 1.42 0.0859 1.26 -2.62
harpacticoida 0.15 -0.131 -0.242 -0.495 -0.954 0.0196 -0.613 0.0931 0.246 -0.00758 -0.226 0.98
hediste_diversicolor 0.41 -4.26 0.506 -0.27 -0.137 1.07 -6.01 1.08 2.73 -5.96 4.93 -1.07
heteranomia_squamula 1 -95.8 -10.4 6.6 -1.75 23.8 -107 -11.8 7.06 -26.8 42.8 10.2
hiatella_arctica 1 -2069 -880 66.6 223 410 -1433 -57.3 319 114 -701 -355
holothuroidea 0.65 -42 2.06 -30.9 -4.33 -136 -1.49 -1.86 3.59 -1.28 -2.83 -0.649
idotea_phosphorea 0.42 -10.7 -4.45 1.46 2.09 -2.41 -0.559 4.09 5.02 -7.25 -3.49 -2.26
ischyroceridae_spp 1 -164 123 -37.8 -77 98.7 -142 -27.2 97.6 -117 37.3 30.2
ischyrocerus_anguipes 1 -319 145 -32.9 -159 125 -185 223 274 -343 38.5 -6.08
isopoda 0 -26.6 9.71e-15 -2.81e-15 -9.5e-15 6.06e-15 5.66e-15 2.43e-15 -1.26e-14 4.18e-15 -7.2e-15 8.98e-15
lacuna_vincta 1 -512 -262 86.7 75.8 43.8 54.4 230 104 -257 -192 -14.6
lamprops_fuscatus 0.19 -2.96 -0.988 -0.577 0.159 -0.551 -2.13 -0.319 0.626 0.418 0.392 0.0473
lamprops_quadriplicata 1 -128 -21.6 -1.94 -38.1 45.3 59.9 1.64 -33.9 -136 71.4 35.9
lepeta_caeca 0.39 -410 -3.95 0.999 1.93 -2204 -1.6 0.939 2.13 -0.0841 -2.69 -2.09
leucon_leucon_nasicoides 0.28 -320 1.61 -0.402 -0.378 -1745 0.324 -0.581 -0.663 -0.364 0.27 0.664
littorina_littorea 0.52 -383 -2.2 1 1.44 -2034 -1.35 4.21 5.35 -5.68 -5.87 -2.6
lumbrineridae_spp 0.73 -35 5.15 -1.2 10.2 -39.1 -28.3 4.43 -1.98 2.06 -1.22 -6.54
lysianassidae_spp 1 -350 -96.8 -250 101 27.2 -249 -6.56 53 -17.1 12.5 -129
macoma_calcarea 0.16 1.64 1.27 -0.459 -0.187 -0.359 -0.0613 -0.443 -0.799 -0.321 0.467 -0.226
maera_danae 1 -646 -267 -134 19.7 1.93 -116 303 422 -593 -137 60.2
maldane_sarsi -6.59 -1.92e+15 -2.39e+14 -2.2e+13 9.55e+14 -1.68e+15 -2.4e+14 -7.47e+14 1.35e+15 -5.59e+14 3.47e+12 -4.07e+14
maldanidae_spp 0.18 -9.24 0.289 -28.9 0.382 -0.868 -0.227 -0.531 0.45 -0.221 -0.202 0.498
monoculopsis_longicornis 0.63 -86.7 -1.56 -28.2 0.0108 -388 1.75 -3.34 4.33 -3.73 -3.27 -1
muculus_musculus_discors 1 -183 -134 -4.48 64.1 -106 5.14 -40.8 62.6 9.69 -19.2 -69.4
mytilus_sp 0.2 -2.88 -0.195 0.148 0.607 -0.934 -1.53 0.538 2.4 -2.36 0.259 -2.23
nematoda 0.47 -2.46 -0.855 -0.28 -0.609 -9.59 1.05 -1.13 -1.24 -2.35 1.62 0.326
nemertea 1 -92.7 -51 26.9 22.7 2.98 -38.2 29.9 30.5 7.02 -28.1 17.9
neoleanira_tetragona 1 -115 4.49 -11.7 -23.4 24.8 41.3 32.9 4.49 -32 -90 -24.2
nephtyidae_spp 0.33 -130 -1.64 -32.4 0.881 -638 1.07 -0.117 -0.174 -3.87 2.61 -0.207
nephtys_caeca 0.35 -374 -0.955 0.485 -0.0885 -2021 -0.971 1.71 -0.0958 1.09 -0.57 -0.714
nephtys_incisa 0.26 -1.32 1.8 0.147 -0.0453 -0.0824 0.75 -1.76 0.237 -0.934 -0.859 0.369
nephtys_sp 0.09 -124 -0.353 -31.1 0.285 -612 0.259 -0.139 0.614 -0.873 -0.243 -0.272
nuculana_minuta 0.16 -325 0.402 0.256 0.451 -1758 -0.758 -0.518 -0.174 -0.675 0.304 -0.531
nymphonidae_spp 1 -95.8 -10.4 6.6 -1.75 23.8 -107 -11.8 7.06 -26.8 42.8 10.2
oenopota_sp 0.32 -4.73 -1.07 0.825 1.73 -0.958 0.288 -0.227 1.85 -5.84 3.17 -1.66
oligochaeta 0.36 -110 0.884 -28.9 0.104 -541 -2.15 0.548 0.613 0.0317 -0.209 1.17
ophelia_limacina 0.17 -364 -1.23 0.642 0.42 -1966 0.302 0.0372 0.753 0.0149 -1.31 0.786
opheliidae_spp 0.6 -135 -1.28 2.39 4.39 -642 4.28 3.63 -2.03 1.84 -11.2 -10.9
ophiopholis_aculeata 1 -382 -167 19.9 171 -728 38.3 -91.9 38.3 1.82 66.6 -207
ophiura_robusta 1 -1451 -896 -28.5 -3.36 311 -324 -168 244 155 -671 -12.7
orchomenella_minuta 1 -96.5 41.7 5.83 24.9 -20 -16.3 -61.4 34.5 0.469 -29.8 17.9
ostracoda 0.2 -1.77 0.218 -0.798 0.196 -1.5 0.757 -0.963 0.922 -0.903 -1.23 -0.232
pagurus_sp 1 -157 -9.45 1.88 25.7 3.61 -99.4 46.6 7.77 5.16 -96.3 -33.5
pagurus_pubescens 0.7 -49.6 -8.77 2.33 -3.38 -9.06 -47.1 -1.85 4.58 -5.28 -1.21 2.49
pandalus_montagui 1 -35.8 -0.149 -5.46 -0.46 2.35 -8.52 -11.2 -0.661 -2.18 15 7.35
parathyasira_equalis 0.4 -28.3 2.88 -26 -1.79 -48.6 -1.19 1.98 -0.646 -2.9 -4.97 -3.97
parvicardium_pinnulatum 0.34 -6.95 -3.92 0.326 2.57 -0.664 -0.914 0.643 2.43 -1.01 -2.06 -3.86
periploma_leanum 0.3 -132 -1.57 -28.8 1.05 -647 0.474 1.38 2.51 -4.71 0.708 0.77
philine_lima 1 -157 -9.45 1.88 25.7 3.61 -99.4 46.6 7.77 5.16 -96.3 -33.5
philomedes_sp 0.3 -331 0.403 0.298 -0.692 -1780 0.817 -0.493 -0.679 -0.419 0.115 -1.46
pholoe_longa -12.23 -3.3e+15 -1.49e+15 7.24e+14 1.38e+15 -7.53e+14 -1.75e+15 6.27e+14 1.94e+15 -4.87e+14 -5.42e+14 -6.12e+14
pholoe_sp 0.17 -0.439 0.829 -0.157 0.0199 -1.01 -1.33 -0.84 0.536 -0.816 1 -0.426
phoxocephalus_holbolli 0.18 -1.72 -0.81 -0.144 -0.105 0.694 -0.591 0.645 -0.0545 -0.254 -0.326 -0.134
polynoidae_spp 0.24 -1.34 2.01 -0.747 -0.661 -0.0722 -0.138 -0.634 -0.544 -0.851 -0.163 0.776
pontogeneia_inermis 1 -114 -50.3 32.4 68.2 -9.71 -45.9 -53.4 99.5 8.83 -19 -6.33
pontoporeia_femorata 0.36 -338 0.279 0.184 0.893 -1835 -1.69 0.418 0.606 0.0448 1.06 0.0201
praxillella_praetermissa 0.22 -10.4 -0.0951 -27.9 0.351 -1.64 0.225 0.0771 0.313 -0.936 0.819 0.226
propebela_turricula 0.16 -127 0.459 -32.1 -0.298 -629 0.0398 -0.808 0.116 -1.62 1.11 -0.167
protomedeia_fasciata 0.31 -286 -0.911 1.22 2.75 -1540 -4.2 0.107 0.9 -0.0794 2.45 -1.89
protomedeia_grandimana 0.33 -1.19 2.01 -0.0472 -0.822 -6.3 -1.32 -1.24 0.52 -1.05 0.78 1.81
puncturella_noachina 1 -92.7 -51 26.9 22.7 2.98 -38.2 29.9 30.5 7.02 -28.1 17.9
quasimelita_formosa 0.15 -1.69 0.709 0.0513 0.495 -1.5 -0.0448 -0.729 0.615 -0.132 -1.5 0.136
quasimelita_quadrispinosa 1 -164 123 -37.8 -77 98.7 -142 -27.2 97.6 -117 37.3 30.2
retusa_obtusa 1 -157 -39.6 22.1 -1.39 27.6 -162 42.3 79.8 30.1 4.63 -16.2
sabellidae_spp 0.32 -10.6 0.201 -29.7 -0.71 1.38 -1.32 1.35 -0.211 -0.353 0.974 0.524
scoletoma_fragilis 0.59 -22.7 -0.434 -13 10.3 2.62 -10.2 1.24 14.3 -13.6 11 -9.35
scoletoma_sp 0.66 -42 -16.6 -24.6 5.96 -59.7 6.13 -4.62 9.75 2.44 -14.1 -10.5
scoloplos_sp 0 -26.6 9.71e-15 -2.81e-15 -9.5e-15 6.06e-15 5.66e-15 2.43e-15 -1.26e-14 4.18e-15 -7.2e-15 8.98e-15
serripes_groenlandicus -2.79 -1.57e+15 -3.25e+14 2.13e+14 -5.27e+13 -1.58e+15 -6.07e+13 1.17e+14 3.94e+14 -1.63e+14 -4.66e+13 1.04e+14
sipuncula 0.2 -11 -0.0619 -30.3 1.61 -0.925 -0.215 -0.00398 0.945 -1.09 0.0207 -0.753
solamen_glandula 0 -26.6 9.71e-15 -2.81e-15 -9.5e-15 6.06e-15 5.66e-15 2.43e-15 -1.26e-14 4.18e-15 -7.2e-15 8.98e-15
solariella_sp 0.63 -15.8 -2.21 1.24 4.69 -20.2 2.72 -2.66 1.35 -0.9 -6.38 -8.38
strongylocentrotus_sp 1 -253 -146 27.6 119 -377 25.6 -55.6 63.1 12.9 0.18 -132
tachyrhynchus_erosus 0 -26.6 9.71e-15 -2.81e-15 -9.5e-15 6.06e-15 5.66e-15 2.43e-15 -1.26e-14 4.18e-15 -7.2e-15 8.98e-15
thracia_septentrionalis 0.13 -1.71 -0.822 0.142 0.366 0.264 -0.0392 0.292 -0.0256 -0.361 0.192 -0.904
thyasira_gouldi 0.19 -1.94 1.1 -0.215 -0.0916 -4.1 0.117 -1.43 0.167 -1.21 0.0981 0.231
thyasira_sp 0 -26.6 9.71e-15 -2.81e-15 -9.5e-15 6.06e-15 5.66e-15 2.43e-15 -1.26e-14 4.18e-15 -7.2e-15 8.98e-15
trichotropis_bicarinata 0.16 -108 0.248 -30.8 0.0429 -510 0.202 -0.253 0.355 -0.0709 -1.67 -1.39
turritellopsis_stimpsoni 0.52 -191 6.82 -1 -6.93 -990 2.76 -2.54 2.35 -5.67 -3.81 1.61
yoldia_myalis 0.07 -347 0.472 -0.0246 -0.687 -1877 0.19 -0.216 -0.394 -0.408 0.414 0.116

Prediction of specific richness based on this model:

Influence indices
McFadden’s pseudo-R2, match ratios and variables coefficients for each taxon
  Pseudo-R2 intercept aquaculture city dredging_collect dredging_dump industry shipping_mooring shipping_traffic sewers_rain sewers_waste wharves_city wharves_industry fisheries_trap fisheries_trawl fisheries_net fisheries_dredge
aceroides_aceroides_latipes 0.36 -2.41 -10.1 -5.22 1.98 8.67 4.37 -4.07 2.92 2.48 -6.14 6.9 -17.1 0.217 -2.9 -1.1 3.11
akanthophoreus_gracilis 0.4 -49 0.876 -1.66 1.11 -3.88 3.21 0.491 2.46 -5.05 5.85 2.39 -2.13 -0.0226 0.0143 -485 1.68
ameritella_agilis 0.67 -12 -4.2 -18.9 4.37 26.8 -4.85 1.53 -9.8 20.4 -17.6 7.36 -28.1 0.961 0.992 -1.18 1.98
ameroculodes_edwardsi -10.88 -2.13e+15 1.51e+15 4.04e+15 1.34e+15 -2e+15 2.31e+15 2.11e+14 1.55e+15 -2.31e+15 2.88e+15 -2.77e+15 -2.11e+15 -6.96e+14 2.1e+13 -7.66e+13 1.9e+14
ampelisca_vadorum 1 -45.9 17.4 -8.25 4.96 1.68 -18.9 -8.32 18 -56 66.1 9.15 -6.09 -36.6 1.05 3.8 -2.15
amphipoda 0.24 -47 -4.23 2.73 0.368 5.33 3.26 -2.54 -0.242 3.18 -3.54 -2.93 -7.4 0.417 0.117 -478 0.391
anonyx_lilljeborgi 0.36 -47.6 -6.82 -16.8 -4.38 3.38 0.728 -3.53 2.86 0.797 -5.44 17.1 -3.69 -0.146 -9.67 -437 -1.99
anthozoa 0 -26.6 -4.49e-15 2.36e-15 -2.95e-15 2.83e-15 6.1e-15 -2.34e-15 8.13e-15 -4.7e-15 4.68e-15 8.62e-16 -1.4e-14 6.28e-16 -3.84e-15 2.1e-17 -1.4e-15
arcteobia_anticostiensis 1 -132 29.9 -44.8 -160 -24.5 -32.5 -1.87 -16.8 -9.97 47.7 64.8 194 -166 -108 5.2 51.2
arrhoges_occidentalis 1 -60.1 108 -1.43 67.8 40.4 -18.7 25.3 14.5 -153 219 -6.41 -125 1.82 6.14 11.5 -18.8
astarte_sp 1 -335 -774 1307 818 437 322 19.7 400 849 -1559 -1404 -1399 -80.6 3.77 25.7 79.9
axinopsida_orbiculata 0.39 -4.35 -9.77 2.46 -8.54 5.18 4.78 -11.1 -0.179 -8.51 5.62 3.27 2.26 0.223 1.24 0.113 -0.671
axiothella_catenata 1 -173 274 438 -41.5 403 -113 267 144 -203 127 -520 -335 2.33 21 43.3 99
bathymedon_longimanus 1 -151 546 253 -76.4 -39.2 -146 183 20.5 -580 800 -237 205 -15.5 1.35 42.9 53
bathymedon_obtusifrons 1 -108 -373 -426 -235 -82.5 213 -281 -98.8 103 -34.1 620 91.4 -14.2 11.8 5.98 40.3
bipalponephtys_neotena 0.28 75.6 -2.51 -1.98 0.619 2.54 3.1 -0.95 0.188 0.0148 0.993 2.74 -6.21 0.582 -0.116 763 1.45
boreochiton_ruber 1 -420 -393 1195 157 444 -242 68.6 20.4 1158 -2138 -1550 41.6 -10.4 14.3 7.98 15.7
brachydiastylis_sp 1 -44 -2.3 9.95 15.7 14 -13.1 -3.47 25.6 -29 26.5 -8.74 -34.8 -35.9 2.49 3.37 17.8
byblis_gaimardii 1 -134 -33.8 -55.4 -42.9 -8.8 -27.7 -60.5 66 -10.6 40.7 75.9 4.93 -284 -1.33 4.65 60.3
cancer_irroratus 1 -239 1113 386 134 -81.5 -465 701 187 -409 637 -597 15.4 32.1 -42.4 4.78 -126
caprella_septentrionalis -7.28 -2.08e+15 3.25e+13 -4.97e+12 -8.07e+13 2.53e+15 -4.73e+14 1.66e+13 -6.1e+14 2.2e+15 -1.97e+15 -2.64e+14 -2.07e+15 -3.87e+14 -4.47e+14 9.01e+13 -2.55e+14
chaetodermatida 0.24 -66.5 4.81 0.236 4.11 -2.92 0.815 2.38 1.52 -0.725 3.27 0.732 -5.1 -0.456 -0.097 -661 0.0733
chionoecetes_opilio 1 -261 -88.1 198 372 1092 272 233 -67.4 780 -960 -444 -1623 32.5 -218 11.9 -117
chlamys_islandica 1 -35.2 -24 -12.6 -14.9 -6.45 11.9 -27.7 -18.1 -19.7 24.5 28.3 31.5 -0.673 10.9 3.76 0.641
chone_sp 1 -71 1.46 -162 3.31 -26.7 74.6 -18.8 -73.1 30 84.6 187 -75.1 7.91 4.79 1.25 0.945
ciliatocardium_ciliatum 1 -57.8 -141 -30.5 -20.2 188 27.1 -129 -21.3 135 -167 18.5 -127 -1.56 -11.9 0.105 -29.6
cirripedia 1 -60.2 31.5 37.9 63.1 -63.3 31.6 32.4 8 -16 39.4 -59.6 -47.7 16.6 0.498 2.28 -17.1
cistenides_granulata 0.38 -75.7 -0.822 -21.6 -0.874 -8.31 -0.0264 9.74 1.62 1.53 -12.4 17.1 8.75 1.02 0.14 -728 -0.476
cossura_longocirrata 1 -74.3 -34.3 -155 125 176 17 136 -64.2 198 -285 70.9 -297 6.96 7.8 0.767 -15.5
crassicorophium_bonellii 1 -62.8 140 -27.7 -15.3 -83.3 -63.6 9.88 6.23 -210 308 42.3 130 -20.2 9.66 10.1 23.4
crenella_decussata 1 -620 -177 406 665 214 -309 1023 285 1324 -3048 -1169 -333 31.5 -44.5 3.09 -96.2
cumacea 1 -61.8 203 15.7 38.4 -70.2 -76.1 105 28.7 -101 171 -41.2 30 3.99 -9.31 -1.21 -34.7
cyclocardia_borealis 0 -26.6 -4.49e-15 2.36e-15 -2.95e-15 2.83e-15 6.1e-15 -2.34e-15 8.13e-15 -4.7e-15 4.68e-15 8.62e-16 -1.4e-14 6.28e-16 -3.84e-15 2.1e-17 -1.4e-15
cyrtodaria_siliqua 1 -118 -416 121 -249 177 99.4 -269 -31.7 293 -441 -66.4 144 -23.5 19.1 9.3 83
diastylis_rathkei 0.22 -45.3 2.95 0.656 -3.01 1.42 -2.65 -1.06 0.532 -4.25 3.57 -1.44 4.92 0.0489 -0.404 -432 -3.25
diastylis_sculpta -8.94 -2.4e+15 -4.77e+13 -3.18e+15 1.99e+14 -2.28e+15 -2.39e+14 1.4e+15 -1.82e+15 -1.82e+14 -1.21e+15 4.18e+15 2.99e+15 2.11e+13 2.7e+14 2.98e+14 -2.21e+14
diastylis_sp 1 -116 -62.1 75.5 -243 236 42.8 -63.9 -148 235 -246 -112 141 9.17 10.4 4.84 -98.6
echinarachnius_parma 0.56 -67.8 -2.19 7.77 2.36 6.5 -11.4 -1.65 -2.28 12.4 -27.4 -12.1 9.52 0.522 0.643 -614 -2.8
edotia_montosa 0.38 -164 -17.9 0.2 -6.44 -9.31 7.69 -10.7 -2.92 6.07 -8.25 6.76 14.1 -12.2 -128 -828 -117
ennucula_tenuis 0.4 -0.232 2.74 -0.83 1.24 -3.7 1.93 1.9 2.05 -3.41 4.56 1.77 -0.943 -0.113 -0.11 0.843 2.22
eteone_sp 1 -1108 388 -1439 -2163 -1514 102 -305 -96.4 -705 1386 2337 2766 -9.65 -5.29 -4263 -402
euchone_sp 1 -108 -373 -426 -235 -82.5 213 -281 -98.8 103 -34.1 620 91.4 -14.2 11.8 5.98 40.3
eudorella_emarginata 0.74 -143 -75.9 -60.3 151 38.1 -4.36 57.2 16.9 -36.1 116 60.2 -236 -7.94 45.3 17 78.3
eudorellopsis_integra 0.84 -13.4 -8 -279 54.4 -33.8 21.3 74.4 18.9 -32.6 -5.67 249 -59.3 -1.36 -1.96 -1.25 11.3
euspira_pallida 1 -271 -686 -63.6 174 1255 260 -561 -122 562 -724 -9.42 -1297 -41.3 -120 39 -72.5
glycera_capitata 1 -71.6 31 92.5 61.8 -119 74.5 43.5 27.1 28.6 -9.76 -119 -53 0.924 -6.03 -0.239 -2.37
glycera_sp 1 -1024 -100 -129 500 2748 -1009 574 -1564 1821 -2684 -907 -797 -208 246 120 -381
goniada_maculata 0.47 -10.4 3.92 -82.1 9.15 -14.2 -1.9 31.2 4.29 -3.46 -19.3 66.8 7.1 -0.312 1.74 0.981 1.5
guernea_prinassus_nordenskioldi 0 -26.6 -4.49e-15 2.36e-15 -2.95e-15 2.83e-15 6.1e-15 -2.34e-15 8.13e-15 -4.7e-15 4.68e-15 8.62e-16 -1.4e-14 6.28e-16 -3.84e-15 2.1e-17 -1.4e-15
halacaridae_spp 1 -35.2 -24 -12.6 -14.9 -6.45 11.9 -27.7 -18.1 -19.7 24.5 28.3 31.5 -0.673 10.9 3.76 0.641
haminoea_solitaria 1 -141 230 274 -365 -154 -59.6 168 18 -66.5 177 -233 537 -17.4 -21.8 11 205
hardametopa_carinata 1 -108 -373 -426 -235 -82.5 213 -281 -98.8 103 -34.1 620 91.4 -14.2 11.8 5.98 40.3
harmothoe_sp 1 -67 71.4 145 77.3 -69.1 46.7 71.7 45 -7.22 13.4 -175 -93.1 6.76 -4.49 8.24 -8.06
harpacticoida 0.33 -60.4 -2.31 -1.17 5.03 -0.517 0.418 -0.447 1.48 -1.32 0.653 2.4 -6.8 0.179 0.0565 -626 -0.0607
hediste_diversicolor -9.37 -1.5e+15 -2.71e+14 6.52e+14 2.14e+15 2.62e+15 -6.66e+14 -2.25e+14 -5.96e+14 1.94e+15 -1.7e+15 -1.22e+15 -3.24e+15 -3.87e+13 -9.89e+13 -3.76e+14 -6.07e+14
heteranomia_squamula 1 -117 -168 251 9.64 151 -34.6 2.43 -48.5 333 -562 -313 27.3 18.7 16.1 3.69 30.8
hiatella_arctica 1 -444 -601 812 -82.7 793 -281 -68 -94.1 1398 -2405 -1166 -4.43 12.6 -248 -6.26 -79.1
holothuroidea 1 -117 -110 176 158 -246 37.9 -3.61 129 -84.3 26 -95.4 -4.36 14.5 21.9 11 49.2
idotea_phosphorea -12.85 -2.57e+15 1.8e+15 -4.62e+13 1.62e+15 3.94e+15 -2.99e+15 1.31e+15 3.26e+14 2.64e+15 -3.85e+15 -1.15e+15 -3.48e+15 -1.86e+14 -6.09e+14 -4.16e+14 -5.69e+14
ischyroceridae_spp 1 -90.8 338 74.9 227 56.9 -175 294 67 -15.9 25.7 -193 -236 -7.45 -15.2 -3.21 1.87
ischyrocerus_anguipes 1 -168 -234 -220 -145 53.8 20.7 -276 -75.8 -170 148 347 123 -213 18.8 32.9 -27.6
isopoda 0 -26.6 -4.49e-15 2.36e-15 -2.95e-15 2.83e-15 6.1e-15 -2.34e-15 8.13e-15 -4.7e-15 4.68e-15 8.62e-16 -1.4e-14 6.28e-16 -3.84e-15 2.1e-17 -1.4e-15
lacuna_vincta 1 -239 1113 386 134 -81.5 -465 701 187 -409 637 -597 15.4 32.1 -42.4 4.78 -126
lamprops_fuscatus 0.3 -66.4 11.4 9.35 3 -6.61 -1.92 8.09 3.4 -5.32 6.13 -10.1 2.93 0.577 -7.86 -639 1.41
lamprops_quadriplicata 1 -224 681 -498 405 245 -126 525 -258 99.5 420 196 -684 -38.7 31.7 -2.81 10.7
lepeta_caeca 1 -888 -430 282 176 -866 62 99.6 101 1038 -2007 525 -137 -46.5 -10.2 22.8 15
leucon_leucon_nasicoides 0.4 -4.47 6.6 -22.5 7.1 -1.32 -2.26 18.8 2.45 4.06 -13.7 12.9 -4.41 -2.45 -0.0532 0.487 0.619
littorina_littorea -7.31 -2.24e+15 6.48e+14 4.01e+15 1.57e+15 3.17e+14 -9.95e+14 1.77e+14 1.32e+15 -6.65e+14 -4.77e+14 -4.45e+15 -1.52e+15 -3.43e+14 -6.62e+14 -2.35e+14 -1.69e+15
lumbrineridae_spp 1 -148 -194 16.2 -11.9 417 98.7 -52.3 -216 529 -619 -171 -230 30.3 13.4 -0.12 -98.4
lysianassidae_spp 1 -116 234 349 48.9 -280 -53.6 127 81.3 -164 146 -359 251 14.1 2.76 10.6 20
macoma_calcarea 0.21 2.24 -3.01 1.14 7.38 3.45 1.77 0.228 0.563 2.78 -5.06 -1.45 -11.4 -0.277 0.245 0.593 1.71
maera_danae 1 -71 1.46 -162 3.31 -26.7 74.6 -18.8 -73.1 30 84.6 187 -75.1 7.91 4.79 1.25 0.945
maldane_sarsi 1 -81.5 -54.1 -105 -330 -3.8 26 -123 -35.5 0.266 85 177 299 -3.82 -11.8 7.32 1.25
maldanidae_spp 0.32 -77.4 4.55 -19.8 4.52 -2.66 -0.715 11.4 0.69 1.69 -4.83 15.3 -3.49 0.203 -0.0626 -774 0.07
monoculopsis_longicornis 1 -172 -390 74.9 552 659 128 -117 46 500 -624 -162 -1230 -2.09 29.6 7.45 -23.6
muculus_musculus_discors 1 -35.2 -24 -12.6 -14.9 -6.45 11.9 -27.7 -18.1 -19.7 24.5 28.3 31.5 -0.673 10.9 3.76 0.641
mytilus_sp 0.35 -64.7 6.41 1.34 -0.17 3.82 -3.55 1.82 -2.77 3.33 -0.776 -2.29 1.98 -0.484 0.232 -631 0.578
nematoda 0.33 -0.248 -1.28 -1.19 1.33 -1.36 0.492 -3.2 2.44 -1.23 2.19 1.85 -3.37 -0.112 -0.673 0.537 0.103
nemertea 1 -67.5 71.3 145 77.3 -69.1 46.7 71.7 45 -7.17 13.3 -175 -93.1 6.77 -4.49 2.73 -8.07
neoleanira_tetragona 1 -113 167 -26.5 271 374 -22.1 254 -53.5 247 -220 -141 -654 -27.8 5.44 0.549 -10.4
nephtyidae_spp -8.94 -1.86e+15 -1.65e+15 1.63e+15 2.19e+14 -1.27e+14 2.03e+15 -1.19e+15 -9.41e+14 2e+15 -1.87e+15 -2.22e+15 -5.91e+14 -2.4e+14 3.98e+14 -2.65e+14 -4.2e+14
nephtys_caeca 0.54 -10.2 21.4 6.18 -9.7 3.27 -14.5 9.34 -0.844 -13.5 11.4 -12.1 19 1.02 -0.739 -0.657 -20.5
nephtys_incisa 0.32 -73.6 -1.62 -26.9 6.13 3.48 1.76 9.42 -0.781 9.01 -16.2 19.9 -9.67 0.152 0.0149 -725 -0.664
nephtys_sp 1 -185 409 -253 -3.95 -60.5 68 197 -37.6 -86.8 353 284 -159 -6.99 -10.6 1.55 -134
nuculana_minuta -4.42 -1.43e+15 4.56e+15 2.32e+15 5.4e+15 1.47e+15 -1.16e+15 5.29e+15 1e+15 2.12e+15 -2.1e+15 -5.12e+15 -7.38e+15 -4.24e+14 -1.54e+14 3.81e+14 7.07e+14
nymphonidae_spp 1 -117 -168 251 9.64 151 -34.6 2.43 -48.5 333 -562 -313 27.3 18.7 16.1 3.69 30.8
oenopota_sp 0.3 -556 6.54 10.1 -6 -0.889 2.12 2.11 -1.71 -1.5 4.89 -9.07 7.18 0.501 -1845 -651 2.19
oligochaeta -10.41 -2.46e+15 -3.79e+15 -1.05e+15 -3.77e+14 1.84e+15 5.26e+14 -1.94e+15 8.97e+14 -3.48e+15 2.33e+15 2.1e+15 -1.52e+15 -6.34e+13 2.72e+14 2.09e+14 1.61e+14
ophelia_limacina 1 -159 406 301 136 5.8 -74.1 274 111 -118 150 -391 -201 -120 -35.7 4.75 -224
opheliidae_spp 1 -453 -225 -997 -1036 -440 298 -1147 -170 -1299 2027 1665 1103 -373 36.4 101 -157
ophiopholis_aculeata -2.79 -2.8e+15 2.67e+15 -4.44e+14 2.28e+15 3.27e+15 1.1e+15 2.53e+15 -2.49e+15 3.58e+15 -1.61e+15 -1.47e+15 -5.81e+15 1.2e+14 4.71e+14 1.53e+14 -8.88e+14
ophiura_robusta 1 -378 -368 792 268 646 -233 66 -131 1156 -2038 -1135 -252 25 7.67 -1.59 -334
orchomenella_minuta 1 -47.7 -66.7 -35.9 72 139 37.1 20.7 -33.5 178 -209 -5.05 -217 1.87 -5.47 -3.41 -3.42
ostracoda 0.26 -48.7 3.73 3.86 5.29 1.73 0.0606 3.34 2.07 -0.749 0.605 -4.58 -8.5 -1.14 -0.115 -488 1.04
pagurus_sp 1 -132 29.9 -44.8 -160 -24.5 -32.5 -1.87 -16.8 -9.97 47.7 64.8 194 -166 -108 5.2 51.2
pagurus_pubescens 1 -231 -319 471 -1.14 178 16.5 43.4 60.4 608 -1147 -638 -17.3 -24 -69 3.26 29.6
pandalus_montagui 1 -108 229 106 -182 181 -127 31.7 11.2 -38.7 136 -167 122 0.809 -17.2 3.29 -29.9
parathyasira_equalis 1 -141 230 274 -365 -154 -59.6 168 18 -66.5 177 -233 537 -17.4 -21.8 11 205
parvicardium_pinnulatum 1 -2498 -231 -2731 -1289 -3011 175 1301 -306 2078 -4166 5085 1573 33.6 -31.8 51.5 -373
periploma_leanum 1 -228 -656 -666 165 427 456 -171 -37.4 486 -645 743 -1161 15.2 -171 11.8 -64.5
philine_lima 1 -132 29.9 -44.8 -160 -24.5 -32.5 -1.87 -16.8 -9.97 47.7 64.8 194 -166 -108 5.2 51.2
philomedes_sp 1 -91.4 -415 -194 -178 -53.7 197 -321 -17.6 68.1 -107 354 75.8 -63.4 5.2 10 30.1
pholoe_longa 1 -108 -373 -426 -235 -82.5 213 -281 -98.8 103 -34.1 620 91.4 -14.2 11.8 5.98 40.3
pholoe_sp 0.25 -56.6 -2.66 2.95 2.48 5.83 0.643 0.519 1.02 5 -8.58 -4.4 -7.86 0.0344 -1.74 -585 1.38
phoxocephalus_holbolli 0.5 66.1 -0.831 10.6 6.73 12.3 -7.64 1.01 1.12 13.3 -22.9 -17.1 -9.15 0.786 -7.37 744 -2.17
polynoidae_spp 0.2 -73.7 -2.53 -2.86 3.45 1.89 1.07 1.27 0.196 5.23 -6.78 1.56 -7.49 -2.59 -1.06 -748 0.203
pontogeneia_inermis 1 -132 -265 -181 -77.2 157 71.7 -276 -46.1 46.9 -30.9 263 -70.4 -189 12 14.5 0.967
pontoporeia_femorata 0.41 -255 0.558 -1.78 -9.96 2.71 -5.83 1.91 2.66 0.559 -0.755 0.447 9.53 0.322 -646 -756 -22.8
praxillella_praetermissa 0.53 -69.7 11.6 -25 -11 -5.42 -2.36 17.4 4.75 -3.62 -0.926 17.4 15.9 0.866 -58.9 -483 5.24
propebela_turricula 1 -379 960 -891 525 809 -311 375 -154 232 654 409 -1388 3.01 -3.92 -15.5 31.9
protomedeia_fasciata 0.62 -30.4 -34 -17.1 -29.4 108 -27.3 -83.3 -17.1 -25.2 26.3 10.6 -3.72 -1.81 3.47 5.95 -6.13
protomedeia_grandimana 0.22 -63.7 -1.91 -3.53 1.52 5.22 0.783 1.01 -0.885 4.9 -5.24 2.58 -7.18 -0.307 -0.217 -660 0.473
puncturella_noachina 1 -67.5 71.3 145 77.3 -69.1 46.7 71.7 45 -7.17 13.3 -175 -93.1 6.77 -4.49 2.73 -8.07
quasimelita_formosa 0.26 -2.37 7.5 -1.15 -0.99 -5.63 1.13 2.32 1.65 -4.32 9.76 4.44 0.379 -0.27 -0.312 0.736 0.213
quasimelita_quadrispinosa 1 -90.8 338 74.9 227 56.9 -175 294 67 -15.9 25.7 -193 -236 -7.45 -15.2 -3.21 1.87
retusa_obtusa -5.68 -2.7e+15 1.32e+15 1.18e+15 2.36e+15 6.96e+15 -2.71e+15 -3.94e+14 -1.02e+15 2.06e+15 -2.78e+15 -2.96e+15 -4.32e+15 9.83e+13 3.33e+14 -1.63e+14 -6.89e+14
sabellidae_spp 0.3 -3.96 -1.39 -0.0106 4.4 3.07 3.85 3.23 -2.91 8.22 -8.36 -3.73 -9.84 1.35 -1.34 -0.575 -2.5
scoletoma_fragilis 0.58 -55.5 -55.8 -148 115 54.6 5.48 32.2 -32.2 88 -87.8 116 -151 -18.3 12.5 0.448 2.83
scoletoma_sp 1 -52.4 -104 35.4 -18.1 -33.5 80.7 -46.5 -11.3 60.2 -82.7 -12.2 -0.625 12 11 3.3 11.4
scoloplos_sp 0 -26.6 -4.49e-15 2.36e-15 -2.95e-15 2.83e-15 6.1e-15 -2.34e-15 8.13e-15 -4.7e-15 4.68e-15 8.62e-16 -1.4e-14 6.28e-16 -3.84e-15 2.1e-17 -1.4e-15
serripes_groenlandicus 1 -559 700 635 -665 -663 135 540 -460 -913 879 -640 1887 -48.5 135 141 -73.3
sipuncula 0.19 -63.6 -1.97 -5.9 0.51 3.15 2.52 1.09 -1.26 4.47 -4.95 4.91 -5.53 0.157 -1.24 -634 -0.143
solamen_glandula 0 -26.6 -4.49e-15 2.36e-15 -2.95e-15 2.83e-15 6.1e-15 -2.34e-15 8.13e-15 -4.7e-15 4.68e-15 8.62e-16 -1.4e-14 6.28e-16 -3.84e-15 2.1e-17 -1.4e-15
solariella_sp 0.61 -133 -44.8 -200 3.86 -20.3 -7.98 -24.3 -9.32 61 -113 227 13.4 -2.58 3.67 -679 -3.62
strongylocentrotus_sp 1 -48.1 -18.1 -36 -9.82 -7.46 -2.27 -50.5 7.26 -81 100 57.7 14.7 -22.8 10.7 6.72 -4
tachyrhynchus_erosus 0 -26.6 -4.49e-15 2.36e-15 -2.95e-15 2.83e-15 6.1e-15 -2.34e-15 8.13e-15 -4.7e-15 4.68e-15 8.62e-16 -1.4e-14 6.28e-16 -3.84e-15 2.1e-17 -1.4e-15
thracia_septentrionalis 0.25 -54.1 9.15 11.2 -0.245 -3.42 -0.804 5.3 1.73 -4.03 4.94 -12.1 2.79 0.726 -0.267 -536 -2.45
thyasira_gouldi 0.35 -95.6 -5.99 -20.5 10.2 2.97 3.48 8.82 -0.377 15.1 -22.8 14.7 -16.4 0.318 -0.117 -968 2.44
thyasira_sp 0 -26.6 -4.49e-15 2.36e-15 -2.95e-15 2.83e-15 6.1e-15 -2.34e-15 8.13e-15 -4.7e-15 4.68e-15 8.62e-16 -1.4e-14 6.28e-16 -3.84e-15 2.1e-17 -1.4e-15
trichotropis_bicarinata 1 -76 -249 -160 -110 -46.5 134 -191 -42.3 66.6 -71.1 275 53.9 -49.9 3.45 4.87 -2.79
turritellopsis_stimpsoni 1 -980 568 2235 819 1251 -408 -555 349 1472 -1592 -2943 -926 -647 -79.3 -13.2 4.47
yoldia_myalis 1 -542 -253 -381 -736 48.6 381 501 198 582 -1324 56.6 427 -84.4 -300 21.6 -27

Prediction of specific richness based on this model:

Density data

Here, we considered density data with a quasi-Poisson distribution.

Abiotic parameters
Influence indices

2.2. Generalized Additive Models

To be added.

2.3. Random Forest Algorithms

To be added.

2.4. Hierarchical Models of Species Communities

First, we initiate the HMSC model with the chosen data, priors and parameters.

HMSC_model <- hmsc(HMSC_data, HMSC_param, HMSC_prior, family = "overPoisson", niter = 100000, nburn = 1000, thin = 100)

Here are the diagnostics to evaluate each model’s quality.

Human activities
Trace plots
Explanatory power
Confidence intervals
Variance partitioning
Habitat parameters
Trace plots
Explanatory power
Confidence intervals
Variance partitioning
All variables
Trace plots
Explanatory power
Confidence intervals
Variance partitioning

Finally, we can predict the values of our parameters within BSI.

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